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Hybrid quantum-classical machine learning offers a path to leverage noisy intermediate-scale quantum (NISQ) devices for drug discovery, but optimal model architectures remain unclear. We systematically optimize the quantum-classical bridge…
The genetic code has been shown to be very error robust compared to randomly selected codes, but to be significantly less error robust than a certain code found by a heuristic algorithm. We formulate this optimisation problem as a Quadratic…
In this paper, we focus on the two-user Gaussian interference channel (GIC), and study the Han-Kobayashi (HK) coding/decoding strategy with the objective of designing low-density parity-check (LDPC) codes. A code optimization algorithm is…
The Gilbert--Varshamov (GV) bound is a classical existential result in coding theory. It implies that a random linear binary code of rate $\epsilon^2$ has relative distance at least $\frac{1}{2} - O(\epsilon)$ with high probability.…
Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…
This paper proposes small tree-width graph decomposition computational protein design CFN instances defined according to the model [1] with protocol defined by Simononcini et al [2] . The proteins used in the benchmark have been selected in…
We prove that $poly(t) \cdot n^{1/D}$-depth local random quantum circuits with two qudit nearest-neighbor gates on a $D$-dimensional lattice with n qudits are approximate $t$-designs in various measures. These include the "monomial"…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
We prove three new lower bounds for graph connectivity in the $1$-bit broadcast congested clique model, BCC$(1)$. First, in the KT-$0$ version of BCC$(1)$, in which nodes are aware of neighbors only through port numbers, we show an…
We wish to minimize the resources used for network coding while achieving the desired throughput in a multicast scenario. We employ evolutionary approaches, based on a genetic algorithm, that avoid the computational complexity that makes…
Inspired by prior work by Tian and by Cao and Xu, this paper presents an efficient computer-aided framework to characterize the fundamental limits of coded caching systems under the constraint of linear coding. The proposed framework…
DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value through screening of libraries with up to billions of unique small molecules. We demonstrate a new…
Clustering is a fundamental tool that has garnered significant interest across a wide range of applications including text analysis. To improve clustering accuracy, many researchers have incorporated background knowledge, typically in the…
In this paper, it is demonstrated that the DNA-based algorithm [Ho et al. 2005] for solving an instance of the clique problem to any a graph G = (V, E) with n vertices and p edges and its complementary graph G1 = (V, E1) with n vertices and…
Particle storage rings are a rich application domain for online optimization algorithms. The Cornell Electron Storage Ring (CESR) has hundreds of independently powered magnets, making it a high-dimensional test-problem for algorithmic…
We examine an error-correcting coding framework in which each coded symbol is constrained to be a function of a fixed subset of the message symbols. With an eye toward distributed storage applications, we seek to design systematic codes…
This work approaches human chromosome mapping by developing algorithms for ordering markers associated with radiation hybrid data. Motivated by recent work of Boehnke et al. [1], we formulate the ordering problem by developing stochastic…
Spatially-coupled (SC) codes, known for their threshold saturation phenomenon and low-latency windowed decoding algorithms, are ideal for streaming applications and data storage systems. SC codes are constructed by partitioning an…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…